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Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication
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Brodel, Andreas K., Jaramillo, Alfonso and Isalan, Mark (2017) Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nature Protocols, 12 (9). pp. 1830-1843. doi:10.1038/nprot.2017.084 ISSN 1750-2799.
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Official URL: http://dx.doi.org/10.1038/nprot.2017.084
Abstract
Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene—or gene circuit function—that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ~7 weeks.
| Item Type: | Journal Article | ||||||
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| Subjects: | Q Science > QP Physiology Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
| Library of Congress Subject Headings (LCSH): | Escherichia coli, Proteins -- Genetic aspects, Transcription factors | ||||||
| Journal or Publication Title: | Nature Protocols | ||||||
| Publisher: | Nature Publishing Group | ||||||
| ISSN: | 1750-2799 | ||||||
| Official Date: | 10 August 2017 | ||||||
| Dates: |
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| Volume: | 12 | ||||||
| Number: | 9 | ||||||
| Page Range: | pp. 1830-1843 | ||||||
| DOI: | 10.1038/nprot.2017.084 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||
| Date of first compliant deposit: | 16 August 2017 | ||||||
| Date of first compliant Open Access: | 10 March 2018 | ||||||
| Funder: | Seventh Framework Programme (European Commission) (FP7), Horizon 2020 (European Commission) (H2020), Engineering and Physical Sciences Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Wellcome Trust (London, England) | ||||||
| Grant number: | FP7-ICT-2013-10 no 610730 EVOPROG, FP7-KBBE no 613745 PROMYS (FP7), Marie Sklodowska-Curie no 642738 MetaRNA (H2020), no BB/M017982/1 (EPSRC) (BBSRC), no WT102944 (Wellcome Trust (London, England)) |
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